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- CAT12.8.1 r1980: 1/1: ./dir_1434256/ds/sub-0367/sub-0367_ses-01_T1w.n
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- SANLM denoising (medium): 173s
- APP: Rough bias correction:
- Initialize 10s
- Estimate background 11s
- Initial correction 24s
- Refine background 5s
- Final correction 11s
- Final scaling 8s
- 79s
- Correct center-of-mass 5s
- Affine registration 22s
- SPM preprocessing 1 (estimate 1 - TPM registration): 116s
- SPM preprocessing 1 (estimate 2): 92s
- SPM preprocessing 2 (write):
- Write Segmentation 27s
- Update Segmentation 30s
- Update Skull-Stripping 66s
- Update probability maps 13s
- 136s
- Global intensity correction: 26s
- SANLM denoising after intensity normalization (medium): 34s
- Fast Optimized Shooting registration 47s
- Local adaptive segmentation (LASstr=0.50):
- Prepare maps 6s
- Prepare partitions 4s
- Prepare segments (LASmod = 1.20) 23s
- Estimate local tissue thresholds (WM) 31s
- Estimate local tissue thresholds (GM) 48s
- Intensity transformation 0s
- SANLM denoising after LAS (medium) 57s
- 174s
- ROI segmentation (partitioning):
- Atlas -> subject space 11s
- Major structures 5s
- Ventricle detection 27s
- Blood vessel detection 16s
- WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 40s
- Manual stroke lesion detection 0s
- Closing of deep structures 2s
- Side alignment 5s
- Final corrections 7s
- 115s
- Blood vessel correction (BVCstr=0.50): 3s
- Amap using initial SPM12 segmentations (MRF filter strength 0.06): 44s
- AMAP peaks: [CSF,GM,WM] = [0.360.05,0.680.08,0.980.05]
- Final cleanup (gcutstr=0.25):
- Level 1 cleanup (ROI estimation) 7s
- Level 1 cleanup (brain masking) 4s
- Level 2 cleanup (CSF correction) 2s
- Level 3 cleanup (CSF/WM PVE) 4s
- 17s
- Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50):
- Template: "/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii"
- 1 | 2.50 | 0.0847 0.0000 0.0847 | 32.0000
- 2 | 2.50 | 0.0818 0.0012 0.0829 | 29.4886
- 3 | 2.50 | 0.0810 0.0018 0.0827 | 26.9772
- 4 | 2.50 | 0.0806 0.0020 0.0826 | 24.6107
- 5 | 2.50 | 0.0803 0.0021 0.0824 | 22.6548
- 6 | 2.50 | 0.0801 0.0021 0.0822 | 20.6989
- 7 | 2.50 | 0.0798 0.0022 0.0820 | 18.9688
- 8 | 2.50 | 0.0796 0.0023 0.0818 | 17.4455
- 9 | 2.50 | 0.0793 0.0023 0.0816 | 15.9223
- 10 | 2.50 | 0.0790 0.0024 0.0814 | 14.6627
- 11 | 2.50 | 0.0787 0.0024 0.0812 | 13.4764
- 12 | 2.50 | 0.0785 0.0025 0.0809 | 12.3015
- 13 | 2.50 | 0.0782 0.0025 0.0807 | 11.3776
- 14 | 2.50 | 0.0779 0.0026 0.0805 | 10.4537
- 15 | 2.25 | 0.0776 0.0026 0.0802 | 9.5920
- 16 | 2.25 | 0.0750 0.0039 0.0789 | 8.8725
- 29 | 2.00 | 0.0768 0.0017 0.0786 | 3.3283
- 30 | 2.00 | 0.0714 0.0040 0.0753 | 3.1221
- 31 | 2.00 | 0.0695 0.0049 0.0744 | 2.9160
- 43 | 1.75 | 0.0690 0.0028 0.0718 | 1.5785
- 44 | 1.75 | 0.0646 0.0052 0.0697 | 1.5194
- 45 | 1.75 | 0.0631 0.0060 0.0691 | 1.4626
- 57 | 1.50 | 0.0623 0.0043 0.0666 | 1.0900
- 58 | 1.50 | 0.0589 0.0065 0.0654 | 1.0730
- 59 | 1.50 | 0.0578 0.0073 0.0651 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 194s
- Prepare output 16s
- 210s
- Jacobian determinant (RMS): 0.010 0.034 0.052 0.078 0.105 | 0.112683
- Template Matching: 0.085 0.225 0.209 0.189 0.173 | 0.173336
- Write result maps: 36s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 38s
- CSF distance: 21s
- PBT2x thickness: 62s
- 128s
- Create initial surface 110s
- Topology correction: 130s
- Surface refinement: 129s
- Reduction of surface collisions with optimization: 91s
- Spherical mapping with areal smoothing 107s
- Spherical registration 337s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 42s
- CSF distance: 21s
- PBT2x thickness: 62s
- 133s
- Create initial surface 109s
- Topology correction: 124s
- Surface refinement: 103s
- Reduction of surface collisions with optimization: 87s
- Spherical mapping with areal smoothing 106s
- Spherical registration 339s
- Final surface processing results:
- Average thickness (FS): 2.4936 0.6665 mm
- Surface intensity / position RMSE: 0.0826 / 0.0933
- Euler number / defect number / defect size: 124.0 / 61.5 / 4.17%
- Display thickness: /var/lib/condor/execute/dir_1434256/ds/sub-0367/surf/lh.thickness.sub-0367_ses-01_T1w
- Display thickness: /var/lib/condor/execute/dir_1434256/ds/sub-0367/surf/rh.thickness.sub-0367_ses-01_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_1434256/ds/sub-0367/sub-0367_ses-01_T1w.nii
- Surface ROI estimation: 10s
- Surface and thickness estimation takes: 2159s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 12s
- ROI estimation of 'neuromorphometrics' atlas 44s
- ROI estimation of 'lpba40' atlas 13s
- ROI estimation of 'hammers' atlas 30s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 11s
- ROI estimation of 'aal3' atlas 18s
- ROI estimation of 'mori' atlas 27s
- ROI estimation of 'anatomy3' atlas 39s
- ROI estimation of 'julichbrain' atlas 51s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 21s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 35s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 82s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 123s
- Write results 124s
- 510s
- Quality check: 8s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_1434256/ds/sub-0367/report/catreport_sub-0367_ses-01_T1w.pdf
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- CAT preprocessing takes 68 minute(s) and 51 second(s).
- Image Quality Rating (IQR): 80.99% (B-)
- GM volume (GMV): 50.47% (757.60 / 1501.09 ml)
- GM thickness (GMT): 2.49 0.67 mm
- Segmentations are saved in /var/lib/condor/execute/dir_1434256/ds/sub-0367/mri
- Reports are saved in /var/lib/condor/execute/dir_1434256/ds/sub-0367/report
- Labels are saved in /var/lib/condor/execute/dir_1434256/ds/sub-0367/label
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